“I will truly miss leading and working side-by-side with these men and women in their pursuit of ATF’s unique law enforcement and regulatory mission,” Jones said in a statement Friday.

President Barack Obama nominated Jones in January 2013, and he was approved by the Senate about six months later.

Outgoing Attorney General Eric Holder praised Jones’ tenure Thursday, saying he “cemented his reputation as an exemplary leader, a consummate professional, and an outstanding public servant.”

“He has made bold changes, advanced forward-looking policies, and taken innovative steps to strengthen ATF’s investigative capabilities_including ballistic imaging technology that recently played a critical role in the investigation of the shooting of two police officers,” Holder said in a statement. “And as a result of Todd’s leadership, ATF has built a proactive, creative, and effective team that is well-prepared to drive the agency into the future.”

Before being approved by the Senate, the former U.S. attorney in Minnesota spent nearly two years as acting director. He was asked to lead the agency after a leadership shake-up in the wake of the failed gun-running investigation known as “Fast and Furious.”

During his confirmation hearing, Jones told lawmakers that the ATF was in “distress” when he took the helm on an interim basis in 2011. At the time, Jones said he was making a variety of changes within the agency to improve its leadership and internal procedures.

Jones was nominated to the post in the aftermath of the December 2012 mass shooting at a Connecticut where 26 people, including 20 children, were killed. The appointment was part of the Obama administration’s efforts to push for tougher gun control laws. Multiple bills failed in Congress, but Jones’ approval was considered a rare victory in the gun control debate.

The Senate had been authorized to approve the ATF’s director since 2006 but never did so before Jones’ confirmation, leaving the agency with a series of interim leaders.

Under Jones’ tenure, the agency faced renewed criticism about its investigative tactics, including the use of so-called storefront and sting operations to pursue violent criminals. Most recently, the agency came under fire for proposing an end to a rule exemption that allowed the sale and manufacture of certain types of bullets used in the popular AR-15-style rifles that could pierce a police officer’s protective fest when fired from a handgun.

The proposed rule change would have effectively outlawed “M855 green tip” or “SS109” rounds with certain types of metal core projectiles. Most of the more than 80,000 public comments about the proposal were critical of the plan, and nearly 300 members of Congress — majorities in both the House and Senate — also complained. The effort was abandoned earlier this month.

Jones’ departure was applauded by the chairman of the House Judiciary Committee, Rep. Bob Goodlatte. The Virginia Republican has been critical of the agency’s management and was among those lawmakers who objected to the ammunition rule change.

“It is clear the ATF needs a change in leadership to repair its tarnished image,” Goodlatte said.